Variant report

Variant	rs12299742
Chromosome Location	chr12:123323357-123323358
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123321572..123324516-chr12:123371831..123374446,2	MCF-7	breast:
2	chr12:123285953..123287953-chr12:123322856..123324793,2	MCF-7	breast:
3	chr12:123321295..123323539-chr12:123344367..123346467,3	MCF-7	breast:
4	chr12:123322572..123324724-chr12:123716443..123718391,2	K562	blood:
5	chr12:123321291..123323892-chr12:123444965..123447071,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10773627	0.88[ASN][1000 genomes]
rs10773657	0.88[ASN][1000 genomes]
rs10847826	0.88[ASN][1000 genomes]
rs10847869	0.88[ASN][1000 genomes]
rs11060064	0.84[ASN][1000 genomes]
rs11060065	0.84[ASN][1000 genomes]
rs11060208	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11060209	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12298151	0.87[ASN][1000 genomes]
rs12298664	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303328	0.82[EUR][1000 genomes]
rs12313006	0.83[ASN][1000 genomes]
rs12314494	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12314544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319654	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12321131	0.84[ASN][1000 genomes]
rs12426809	0.88[ASN][1000 genomes]
rs1532835	0.86[ASN][1000 genomes]
rs1587856	0.80[ASN][1000 genomes]
rs1671685	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1696326	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1696349	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1799618	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1979236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1979237	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2100500	0.98[ASN][1000 genomes]
rs2135014	0.86[ASN][1000 genomes]
rs2271051	0.85[ASN][1000 genomes]
rs2292131	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292132	0.86[ASN][1000 genomes]
rs2292134	0.84[ASN][1000 genomes]
rs2292135	0.83[ASN][1000 genomes]
rs2292136	0.82[ASN][1000 genomes]
rs2292138	0.80[ASN][1000 genomes]
rs2292139	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2343108	0.86[ASN][1000 genomes]
rs2343109	0.80[ASN][1000 genomes]
rs2343685	0.88[ASN][1000 genomes]
rs2649908	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649909	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2880678	0.88[ASN][1000 genomes]
rs3817094	0.85[ASN][1000 genomes]
rs3852536	0.84[ASN][1000 genomes]
rs4759355	0.93[ASN][1000 genomes]
rs4759389	0.88[ASN][1000 genomes]
rs56272219	0.98[ASN][1000 genomes]
rs58182048	0.84[ASN][1000 genomes]
rs59192320	0.85[ASN][1000 genomes]
rs59922385	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60308342	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7138398	0.80[ASN][1000 genomes]
rs7303024	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73421642	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs735378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7398546	0.82[ASN][1000 genomes]
rs754080	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs897385	0.80[ASN][1000 genomes]
rs897386	0.80[ASN][1000 genomes]
rs897391	0.88[ASN][1000 genomes]
rs897392	0.88[ASN][1000 genomes]
rs897393	0.88[ASN][1000 genomes]
rs921808	0.90[ASN][1000 genomes]
rs936083	0.82[ASN][1000 genomes]
rs937520	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs937766	0.86[ASN][1000 genomes]
rs9788290	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123321400-123323600	Active TSS	Rectal Smooth Muscle	rectum
2	chr12:123321400-123324400	Weak transcription	Lung	lung
3	chr12:123321600-123323400	Flanking Active TSS	Fetal Intestine Large	intestine
4	chr12:123321600-123324400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123321600-123324400	Weak transcription	Right Ventricle	heart
6	chr12:123321600-123324400	Weak transcription	NHLF	lung
7	chr12:123321600-123324600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:123321600-123324600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:123321600-123324600	Weak transcription	Psoas Muscle	Psoas
10	chr12:123321600-123324600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:123321600-123324600	Weak transcription	HSMM	muscle
12	chr12:123321600-123325000	Enhancers	Fetal Brain Male	brain
13	chr12:123321600-123325000	Weak transcription	NH-A	brain
14	chr12:123321600-123325600	Weak transcription	Placenta	Placenta
15	chr12:123321600-123325600	Weak transcription	Osteobl	bone
16	chr12:123321600-123326400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:123321600-123327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:123321600-123332800	Weak transcription	Ovary	ovary
19	chr12:123321600-123333000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:123321800-123323400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:123321800-123323600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr12:123321800-123323600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:123321800-123323600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:123321800-123323600	Weak transcription	Small Intestine	intestine
25	chr12:123321800-123323800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:123321800-123324400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:123321800-123324400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:123321800-123324600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:123321800-123324600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:123321800-123324600	Weak transcription	NHDF-Ad	bronchial
31	chr12:123321800-123324800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr12:123321800-123324800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:123321800-123325000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:123321800-123325200	Enhancers	HMEC	breast
35	chr12:123321800-123325800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:123321800-123325800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:123321800-123325800	Enhancers	Colonic Mucosa	Colon
38	chr12:123321800-123326200	Enhancers	Brain Anterior Caudate	brain
39	chr12:123321800-123336800	Weak transcription	Aorta	Aorta
40	chr12:123322000-123323400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:123322000-123324400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:123322000-123324600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:123322000-123324800	Enhancers	Brain Substantia Nigra	brain
44	chr12:123322000-123332400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:123322200-123323400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr12:123322400-123323400	Enhancers	Left Ventricle	heart
47	chr12:123322400-123323600	Enhancers	Esophagus	oesophagus
48	chr12:123322400-123323600	Enhancers	Stomach Mucosa	stomach
49	chr12:123322400-123325800	Weak transcription	Fetal Heart	heart
50	chr12:123322400-123329000	Weak transcription	Thymus	Thymus

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